I want to perform pairwise alignment and get the resulting CIGAR string.

The channel can emit insertions, deletions and substitution errors.

For example, if the input was AAGCT

Then the output could be AAAAGGC

Where there were the following errors in the following positions.

1, Insertion of A at first position 2, Insertion of A at second position 3, Insertion of G at the third position 4, Deletion of T at the last position

I want to know how I could obtain the CIGAR string given two sequences. In addition, could I use viterbi algorithm for this?

  • $\begingroup$ What's your question? $\endgroup$
    – user438383
    Dec 2 '20 at 9:05
  • $\begingroup$ How to obtain CIGAR string given two sequences $\endgroup$ Dec 2 '20 at 14:22

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